Gene regulation during submergence stress response in diverse plant species

REYNOSO MAURICIO ALBERTO; PAULUZZI, GERMAIN; BAILEY-SERRES, JULIA; BAJIC, MARKO; WEST, DONNELLY A.; SINHA, NEELIMA; KAJALA, KAISA; BRADY, SIOBHAN M.; DEAL, ROGER B.

Georgia

Simposio; Suddath Symposium, "Epigenetics: From Mechanisms to Tree of Life"; 2019

Plants are stationary organisms that must constantly respond to a changing environment in order to survive. Primary detection and response toflood stress occurs in the roots. However, how the specific cell types of the roots respond to these stresses is not completely understood. Wehave utilized two techniques, INTACT (Isolation of Nuclei TAgged in specific Cell Types) and TRAP (Tagged Ribosome Affinity Purification), toisolate nuclei and translating ribosomes from the root tip of four plant species: Oryza sativa (rice), Medicago truncatula (clover), Solanumlycopersicum (domesticated tomato), and Solanum pennellii (wild type tomato). We used ATAC-seq (Assay for Transposase-Accessible Chromatinsequencing) to characterize chromatin accessibility changes in root tips in response to 2 hours of submergence. Additionally, we performed RNAsequencing using nuclear RNA, total mRNA, and translating mRNA to characterize the transcriptional and translational response to submergencestress. Submergence stress is perceived differently in each species but our comparison of gene families up-regulated in any RNA populationidentified a conserved set of Submergence UpRegulated orthologous gene Families (SURFs) present in all four species. Conserved SURFs showedaccessible chromatin across their gene bodies during submergence stress. Additionally, promoters of SURFs contained overrepresented motifsthat are also found in Transposase Hypersensitive Sites (THSs) with increased accessibility during submergence. Four of these TF-bindingsequence motifs are found more frequently in SURF gene promoters, compared to all other genes, in all four species. Interestingly, increasednumbers of motifs within a promoter correlated with increased gene expression, but this correlation is more significant if the motif is locatedinside an accessible site. These four motifs represent evolutionarily conserved regulators of gene expression that are induced through hypoxia.Further work will focus on characterizing the kinetics of this response and what proteins bind these elements. The long-term goal of this researchis to identify the regulators of submergence stress in plants and to apply these targets for making hardier crops.